The application of chemical fertilizers and organic fertilizers, as well as irrigation, is an important agricultural practice that can increase crop yields and affect soil biogeochemical cycles. This study conducted coconut field experiments to investigate the effects of conventional fertilization (NCF), optimized fertilization (MCF), conventional fertilization + organic fertilizer (NOF), optimized fertilization + organic fertilizer (MOF), conventional fertilization + organic fertilizer + irrigation (NOFW), and optimized fertilization + organic fertilizer + irrigation (MOFW) treatments on soil physicochemical properties, soil enzyme activity, bacterial and fungal community structure and diversity, and compared the controls (CK, non-fertilizer and non-irrigation). The results showed that MOFW significantly increased soil electrical conductivity (EC), organic matter (OM), alkaline nitrogen (AN), available phosphorus (AP), available potassium (AK), available calcium (ACa), and available magnesium (AMg) levels. At the same time, it also significantly enhanced the activities of soil catalase (CE), polyphenol oxidase (POE), sucrase (SE), urease (UE), acid protease (APE), and acid phosphatase (APPE) (p < 0.05). The PCA analysis of soil microorganisms in the coconut rhizosphere soil showed indicated significant changes in bacteria and fungi community structure under fertilization treatments. The fertilization application leaded to an increase in the relative abundance and diversity of bacteria, but a decrease in fungi. Acidobacteriota, Proteobacteria, and Actinobacterota were the dominant bacterial phyla, and Ascomycota, Basidiomycota, Rozellomycota, and Mortierellomycota were the significant fungal phyla. Compared with CK, MOFW significantly increased the abundance of Acidobacteriota, Proteobacteria, Basidiomycota, and Mortierellomycota. Redundancy analysis (CCA) and Mantel test further revealed that pH, EC, OM, and AP were the main soil fertility factors driving changes in microbial communities. CE, SE, UE, APE, APPE were significantly correlated with microbial communities. Compared with NOFW, MOFW has a lower proportion of N, P, and K fertilizers in its fertilizer composition. The results indicated that MOFW can better improve the nutrient and enzyme status of the soil, which is a promising method for maintaining the balance of soil microorganisms in coconut orchards, and accordingly, reducing chemical fertilizers within a certain range can not only ensure consistency with conventional fertilizers, but also effectively improve soil conditions.